Contacts of the strand formed by residues 404 - 411 (chain A) in PDB entry 4NTX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 404 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A LEU* 3.7 25.4 - - + -
222A MET* 4.0 26.2 - - + -
223A LEU 3.4 5.2 - - - +
224A ASP* 3.9 15.7 - - + +
269A GLY* 2.7 34.3 + - - -
380A ILE* 3.9 27.1 - - + +
389A LEU* 5.2 2.7 - - + -
393A TYR* 5.9 0.9 - - + -
395A LYS* 6.3 0.2 - - + -
399A TYR* 4.7 1.8 - - + -
400A ILE* 3.0 51.7 + - + +
403A ASN* 1.3 86.1 - - + +
405A LEU* 1.3 59.6 + - - +
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Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ILE 4.8 0.2 - - - +
222A MET* 3.4 4.2 - - - +
223A LEU* 2.9 52.2 + - + +
225A ILE* 3.8 26.7 - - + -
246A ILE* 4.2 20.6 - - + +
266A VAL* 4.1 22.9 - - + +
267A ALA 3.6 26.0 - - - +
268A PRO* 4.0 2.2 - - + -
270A PHE 3.4 14.4 - - - +
380A ILE* 4.4 1.8 - - - -
404A ILE* 1.3 75.0 - - - +
406A VAL* 1.3 77.3 + - - +
407A LEU* 4.3 8.7 - - + +
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Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLU* 3.6 23.3 - - + +
221A ILE 3.2 10.3 - - - +
222A MET* 3.6 35.0 - - + -
266A VAL* 5.0 0.2 - - - +
270A PHE 3.1 7.3 + - - +
271A GLN* 3.3 18.8 - - + +
272A THR* 2.8 28.2 + - - -
380A ILE* 3.7 17.5 - - + -
405A LEU* 1.3 81.4 - - - +
407A LEU* 1.3 63.9 + - - +
408A ASP* 3.6 17.7 - - - +
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Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A VAL* 5.3 2.0 - - + -
93A PHE* 5.9 1.1 - - + -
219A LEU* 3.6 3.3 - - + +
220A GLU* 3.2 4.2 - - - -
221A ILE* 2.8 59.0 + - + +
246A ILE* 4.5 6.7 - - + -
248A VAL* 4.1 25.1 - - + -
264A PHE* 5.0 0.9 - - + -
266A VAL* 4.0 17.7 - - + -
272A THR* 3.6 14.1 - - - +
274A VAL* 3.8 22.2 - - + -
405A LEU* 4.3 10.3 - - + +
406A VAL* 1.3 76.2 - - - +
408A ASP* 1.3 64.4 + - - +
409A ILE* 3.9 25.0 + - + -
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Residues in contact with ASP 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A THR* 3.7 17.7 + - - +
219A LEU 3.2 5.9 - - - +
220A GLU* 2.7 32.6 - - - +
271A GLN* 2.8 34.7 + - - +
272A THR 3.0 11.5 + - - +
273A PHE* 4.0 19.6 - - + -
274A VAL* 2.9 30.5 + - - +
406A VAL* 3.6 4.0 - - - +
407A LEU* 1.3 75.8 - - - +
409A ILE* 1.3 62.0 + - - +
410A PHE* 3.9 5.9 - - + -
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Residues in contact with ILE 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PHE* 3.4 20.9 - - + -
89A PRO* 5.4 1.8 - - + -
91A VAL* 3.8 33.2 - - + -
218A GLY* 3.3 2.1 - - - -
219A LEU* 2.8 43.7 + - + -
248A VAL* 4.5 4.0 - - + -
250A ILE* 3.6 33.7 - - + -
264A PHE* 4.8 0.7 - - + -
274A VAL* 3.6 14.8 - - + +
276A CYS* 4.0 10.1 - - - -
407A LEU* 3.9 26.6 - - + -
408A ASP* 1.3 77.7 - - - +
410A PHE* 1.3 64.0 + - - +
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Residues in contact with PHE 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PHE* 4.5 5.4 - - - -
214A GLY* 3.5 33.2 - - - +
215A THR* 3.7 27.6 - - - +
217A ASN 4.9 0.2 - - - -
218A GLY* 4.0 12.8 - - - -
219A LEU 5.8 0.2 - - - +
273A PHE* 4.2 23.6 - + + -
274A VAL 3.3 25.5 + - - +
275A SER* 3.6 31.4 - - - -
276A CYS* 2.8 27.1 + - - +
408A ASP* 3.9 9.6 - - + -
409A ILE* 1.3 79.2 - - - +
411A PHE* 1.3 71.4 + - - +
412A GLU* 5.0 1.6 - - - -
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Residues in contact with PHE 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 3.9 27.1 - - + -
87A THR 4.2 11.0 - - - -
88A PHE* 4.1 11.0 - + - -
89A PRO* 3.9 31.6 - - + -
210A THR* 4.1 28.3 - - + +
212A LYS 4.5 1.7 + - - +
213A GLY* 3.4 1.9 - - - -
214A GLY 2.7 33.4 + - - -
276A CYS* 3.4 31.0 - - + -
278A GLU* 4.1 19.5 - - + -
371A TYR* 3.9 24.0 - + - -
410A PHE* 1.3 80.5 - - - +
412A GLU* 1.3 56.7 + - - +
413A ALA 3.9 14.4 - - - +
414A LEU* 5.4 0.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il